GateTool Functions of Super Segger

All clist management and data visualization can be completed using the gateTool function. The gateTool function is organized to intake a clist, and a combination of commands and arguments. The clist can be input as a clist, clist cell array, directory, or filename.

Below we list the command string options, as well as the arguments which must be passed with each command. For a more in-depth tutorial of how to pass commands and arguments into the gateTool, we have an extensive tutorial which teaches you how to use this flexible data analysis tool : http://mtshasta.phys.washington.edu/website/gatetoolTutorial/tutorial.html.

Clist modification commands:

'merge' : Merges all input clists into a single output clist (no arguments needed)

'name', str : Labels input clist(s) with the name str; now when this data is plotted, the legend will you this name to label the data

'color', cc : Set color cc for all clist data to be plotted in

'strip' : Remove all un-gated cells (no arguments)

'make', ind : Gate on indices in ind. Specify either 1 or 2 as a vector index names are stored in def and can be view by running the def command. If the ind is a structure it assumes it is a preformed gate and adds it to the gate array in all clists. Any gating is performed on all clists input.

'squeeze' : make a clist vertical so all entries are treated as identical conditions. when a gate is applied, it will be applied to all squeezed clists identically

'expand' : make a clist horizontal so all entries are treated as different conditions

'add', data, name : add a field (name) to the clist data with values (data)

'add3D' data, name : add a field (name) to the 3D (time-dependent) clist data with values (data)

'get', index : gets data from data column index

'getgate', index : gets the indexed gate

Visualization commands:

'show', ind : This command will make a figure for viewing without modifying the clist. ind is either and index or pair of indices specifying what is to be visualized. If no ind is passed then all gates are displayed on a single clist input

'kde' : Make either a 1 or 2D KDE (depending on dimension of ind) 'show' must be called as well.

{'time','3D'} : Make a temporal plot of single cell dynamics for one index 'show' must be called as well.

'hist' : Make a 1 or 2D histogram (depending on dimension of ind) 'show' must be called as well.

'dot' : Make a dot plot. Dim of ind must equal 2. 'show' must be called as well.

'log', axes : Set of axes to set with log scales. axes = [1,2,3] will set x, y and color axis to have log scale.

'den' : Normalize KDE and hist like a probability density

'cond' : Normalize like a conditional probability density

'no clear' : Do not run clear figure (clf) before drawing.

'rk', rk : radius of the gaussian kernel for KDE

'rm', rm : radius of the point mask for KDE

'inv' : invert 2D hist/KDE image for printing

'mult', mult : set the resolution for the KDE. Set the number of pixels in the image created to make ke

'bin', bin : set the binning for the hist and KDE. In 1D, if bin is a scalar it is interpretted as the number of bins. If it is a vector it is assumed to be the bin centers. In 2D, if bun is a vector, it is interpretted to be a vector of bin numbers for the two dimensions. If it is a cell array, it is assumed to be two vectors of centers.

'err' : show error in 1D histograms and kde's

'stat' : show statistics for a show command. Only one index.

'newfig' : draws new figures for each clist

Other commands:

'def' : Show all the channel definitions at the command line

'def3D' : Show all the temporal channel definitions at the command line

'xls', filename : export an excel doc with the clist data. Need to have excel installed to export.

'csv', filename, [ind] : export a csv doc with the clist data.

'save', filename : Save .mat file.

'units', units : set the multiplier for the data to set the desired units

'drill' : Use recursive loading through a directory tree to any level.

Some Examples

Adding your own variables (cell descriptors) to the Clist

• You can customize your Clist by adding your own variables to the Clist
• If you have a vector representing that variable (i.e. mean intensity of fluorescence in a fifth channel) you can add your values to the Clist using the gateTool function and the 'add' option clist_edited = gateTool(clist_old, 'add', yourVariable, "Name for Your Variable"
• For example, if I have Clist "clist" and vectors of fluorescence "fluor5" I can add these values as the next row to make a new clist containing that variable: clist_withFluor5 = gateTool(clist, 'add', fluor5, 'Mean Intensity of Channel 5 Fluorescence' );
• For more examples of this and all other features of the gateTool, please see the gateTool online tutorial at: http://mtshasta.phys.washington.edu/website/gatetoolTutorial/tutorial.html